The timing of Khan's arrest -- months after his indictment and years after his last alleged criminal act of assisting an attacker in a deadly 2009 assault in Pakistan -- is one of the mysteries in the case against the 48-year-old engineer. The delays were central to a federal judge's finding that Khan was not a threat to the community and should be released from custody pending trial.

Khan has pleaded not guilty to one count of conspiracy to provide material support to terrorists.

Assistant U.S. Attorney Ethan Knight and an FBI spokeswoman declined to comment on the case.

Court hearings and legal experts offer some insight on the government's actions. But some said they are surprised at what has been revealed so far in a case that may brew for months or years.

Release on bond

The judge's decision to release Khan from custody on $25,000 bond, a relatively low amount, shocked Jeff Addicott, director of the Center for Terrorism Law at St. Mary's University School of Law.

"The $25,000 bond is not consistent with the charge," Addicott said, calling the amount "offensive." The material support charge is "the most serious charge in our arsenal against terrorism short of murder," he said.

But in custody hearings last week, the government could not prove to the satisfaction of two federal judges that Khan was a danger or a flight risk that could only be controlled by jailing him. They noted the delay in arresting him as well as the lack of any ongoing suspicious activities justifying keeping him in custody.

Knight, the prosecutor, acknowledged the charges were "of a historical nature" and did not cite any behavior since 2009 that concerned the government.

The government's insistence that Khan is an ongoing threat without having allegations to support that assertion is "somewhat curious," said Greg McNeal, a Pepperdine University professor who specializes in national security law, about the lack of activity since 2009. If the government can't show more recent activity, he said, the defense could argue that there is an innocent explanation for Khan's actions.

The government's inability to make the case for holding Khan could have an impact on public perceptions, McNeal said. The risk, he said, is that people will start to wonder, "'If the guy is not even dangerous enough to be required to go to jail, is this really the type of person we should be using federal resources to prosecute?'"

Much remains to be seen about the government's case.

It's possible that federal prosecutors lack evidence to show that Khan is an extremist that the charge against him would suggest, Addicott said. Perhaps Khan provided support as a family favor, Addicott said, although it remains unclear how they knew each other.

"Family relationships are very tight in the Muslim world," he said. "He could have had some family obligation hovering over him."

An attack in Pakistan

On May 27, 2009, three men launched an armed assault against the Inter-Services Intelligence headquarters in Lahore, Pakistan. The attack killed about 30 people and injured 300 others.

The federal government has not disclosed when its investigation into Khan began. But through emails and other evidence obtained under the Foreign Intelligence Surveillance Act, the government began building a conspiracy case against Khan, alleging he exchanged emails since at least late 2005 with one of the three attackers -- a man from the Maldives known as Ali Jaleel.

The indictment cites portions of emails between Jaleel and Khan about Jaleel's plans to go to Pakistan and asking Khan to care for Jaleel's family.

The three-and-a-half year period between the attack and the charges is not surprising, said McNeal. Often, once investigators are following a terror suspect, they will wait before sweeping in, he said.

Less clear is why the federal government would wait to arrest Khan after securing its indictment.

In court, Knight would say only that law enforcement was making "tactical decisions" about when to arrest Khan.

One possibility, said Tung Yin, a Lewis and Clark Law School professor and expert in terrorism and the law, is coincidental timing with another major Portland terrorism case.

Yin noted that the Khan indictment was returned on December 27, 2012 -- two weeks before jury selection began for the trial of Mohamed Mohamud, accused of attempting to set off a bomb at a Pioneer Square Christmas tree lighting in 2010.

The federal government may have been concerned that arresting Khan and media coverage accompanying a terrorism arrest could taint the jury pool for the Mohamud trial, Yin said.

Prosecutors could face criticism or otherwise be penalized by the judge if he felt they were trying to influence the Mohamud trial, he said.

The lead prosecutor in the Mohamud trial, as in the Khan case, is Knight.

But that is likely only one of the reasons, Yin said. And, as with other elements of the case that remain shrouded in mystery, time may or may not tell.